Aneuploidy-Dependant Massive Deregulation of the Cellular Transcriptome in Human Rectal and Colon Carcinomas In order to identify genetic alterations underlying rectal carcinogenesis, we used global gene expression profiling of a series of 17 locally advanced rectal adenocarcinomas and 20 normal rectal mucosa biopsies on oligonucleotide arrays. A total of 351 genes were differentially expressed (p less than 1.0e-7) between normal rectal mucosa and rectal carcinomas, 77 genes had a greater than five-fold difference, and 85 genes always had at least a two-fold change in all of the matched samples. 12 genes satisfied all three of these criteria. Altered expression of genes such as PTGS2 (COX2), WNT1, TGFB1, VEGF and MYC were confirmed, while our data for other genes like PPARD and LEF1 were inconsistent with previous reports. In addition, we found deregulated expression of many genes whose involvement in rectal carcinogenesis has not been reported. By mapping the genomic imbalances in the tumors using comparative genomic hybridization, we could show that DNA copy number gains of recurrently aneuploid chromosome arms 7p, 8q, 13q, 18q, 20p and 20q correlated significantly with their average chromosome arm expression profile. Taken together, our results demonstrate that both the high-level, significant transcriptional deregulation of specific genes and general modification of the average transcriptional activity of genes residing on aneuploid chromosomes coexist in rectal adenocarcinomas. In order to characterize patterns of global transcriptional deregulation in primary colon carcinomas, we performed gene expression profiling of 73 tumors (UICC stage II, n=33 and UICC stage III, n=40) using oligonucleotide microarrays. For 30 of the tumors, expression profiles were compared to those from matched normal mucosa samples. We identified a set of 1,950 genes with highly significant deregulation between tumors and mucosa samples (P less than 1e-7). A significant proportion of these genes mapped to chromosome 20 (P=0.01). Seventeen genes had a greater than five-fold average expression difference between normal colon mucosa and carcinomas, including up-regulation of MYC and of HMGA1, a putative oncogene. Furthermore, we identified 68 genes that were significantly differentially expressed between lymph node negative and positive tumors (P less than 0.001), the functional annotation of which revealed a preponderance of genes that play a role in cellular immune response and surveillance. The microarray-derived gene expression levels of 20 deregulated genes were validated using quantitative real-time RT-PCR in more than 40 tumor and normal mucosa samples with good concordance between the techniques. Finally, we established a relationship between specific genomic imbalances, which were mapped for 32 of the analyzed colon tumors by comparative genomic hybridization, and alterations of global transcriptional activity. Previously, we had conducted a similar analysis of primary rectal carcinomas. The systematic comparison of colon and rectal carcinomas revealed a significant overlap of genomic imbalances and transcriptional deregulation, including activation of the Wnt/b-catenin signaling cascade, suggesting similar pathogenic pathways. A similar deregulation was also observed in another series of colorectal carcinomas, in which we were able to follow the sequence of transformation from normal epithelium, early low-grade adenoma, late high-grade adenoma, invasive carcinomas and their associated metastases. In order to identify sequential alterations of the genome, transcriptome, and proteome that define the transformation of normal epithelium and the progression from adenomas to invasive disease, we have analyzed tissue samples from 20 normal mucosa specimen, 12 adenomas, 18 primary sporadic colorectal carcinomas, and 12 liver metastases. Included in this collection were samples of the mucosa-adenoma-carcinoma sequence from 17 individual patients. Confirming previous studies, comparative genomic hybridization (CGH) revealed patterns of stage specific, recurrent genomic imbalances. Gene expression analysis was performed on 9K cDNA arrays. T-test group comparison identified 58 genes differentially expressed between normal mucosa and adenoma, 118 genes between adenoma and carcinoma, and 163 genes between primary carcinoma and liver metastasis (p less than 0.001). Expression levels of 1750 genes increased constantly from normal mucosa to adenoma and carcinoma, whereas 2099 genes showed decreased expression levels. The differentially expressed genes belong to cellular pathways involved in death receptor signaling, inhibition of apoptosis, and p53-, TNF-alpha-, NF-K beta-, TNFR1-, and integrin-signaling. The parallel analysis of our samples using both CGH and expression profiling allowed establishing a direct correlation of chromosomal copy number changes and chromosome specific average gene expression levels for chromosomes 7, 13, 17, 18, and 20 (p less than 0.01). Protein expression patterns of a subset of the samples were analyzed by 2-dimensional gel electrophoresis and subsequent mass spectrometry. While there was no direct match of the 42 differentially expressed proteins and sequences on the array, most of the differentially expressed genes and proteins belonged to identical pathways or networks. In conclusion, increasing genomic instability and a recurrent pattern of chromosomal aberrations as well as distinct gene- and protein expression patterns correlate with distinct stages of colorectal cancer progression. Chromosomal aneuploidies exert a direct effect on average expression levels of the genes residing on the aneuploid chromosomes thereby contributing to a massive deregulation of the cellular transcriptome. This aneuploidy-dependent transcriptional deregulation is not specific for colon cancer, as we have observed a similar phenomenon in primary breast cancer as well. The nuclear topography of aneuploid chromosomes and their consequences on transcriptional activity Chromosomal aneuploidy is a defining feature of the vast majority of carcinomas. In non-hereditary forms of colon cancer, additional copies of chromosomes 7, 13 and 20 are not only observed in early pre-dysplastic lesions, but are faithfully maintained throughout progression to metastasis. It has been established that chromosomes assume a well conserved 3-dimensional positioning within the interphase nucleus. An increase in chromosome copy number has also been shown to correlate with an overall increased expression of genes residing on that chromosome. We are therefore performing 3-dimensional fluorescence in situ hybridization (3D-FISH) on cell lines containing artificially derived trisomies to determine if this increased expression required the aneuploid chromosome to adopt the same nuclear position, as its endogenous homologues. Our results demonstrate that endogenous chromosome 7 and 18 territories are peripheral in position, while chromosome 19 territories are centrally localized. Remarkably, the artificially introduced trisomic chromosomes are positioned identically to their endogenous counterparts in the colon cancer cell line DLD-1. Our data is therefore consistent with the idea that inherent to each chromosome is a zip code th [summary truncated at 7800 characters]